Merge pull request #20 from monarch-initiative/duckdb-update

Update to duckdb 0.10.2, fix casting of boolean to string (likely due to better auto-typing in duckdb's read_csv).
monarch-initiative · Apr 26, 2024 · e8715fe · e8715fe
2 parents 1df1308 + 384049a
commit e8715fe
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Showing 3 changed files with 56 additions and 57 deletions.
diff --git a/closurizer/closurizer.py b/closurizer/closurizer.py
@@ -57,16 +57,18 @@ def node_joins(predicate):
         on {field}_edges.object = {field}_closure_label.id
     """
 
+
 def grouping_key(grouping_fields):
     fragments = []
     for field in grouping_fields:
         if field == 'negated':
-            fragments.append(f"coalesce({field}.replace('True','NOT'), '')")
+            fragments.append(f"coalesce(cast({field} as varchar).replace('true','NOT'), '')")
         else:
             fragments.append(field)
     grouping_key_fragments = ", ".join(fragments)
     return f"concat_ws('|', {grouping_key_fragments}) as grouping_key"
 
+
 def add_closure(kg_archive: str,
                 closure_file: str,
                 nodes_output_file: str,

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -8,7 +8,7 @@ authors = ["Kevin Schaper <[email protected]>"]
 python = "^3.8"
 click = "^8"
 SQLAlchemy = "^1.4.37"
-duckdb = "^0.9.1"
+duckdb = "^0.10.2"
 
 [tool.poetry.dev-dependencies]